1
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Warner BB, Rosa BA, Ndao IM, Tarr PI, Miller JP, England SK, Luby JL, Rogers CE, Hall-Moore C, Bryant RE, Wang JD, Linneman LA, Smyser TA, Smyser CD, Barch DM, Miller GE, Chen E, Martin J, Mitreva M. Social and psychological adversity are associated with distinct mother and infant gut microbiome variations. Nat Commun 2023; 14:5824. [PMID: 37726348 PMCID: PMC10509221 DOI: 10.1038/s41467-023-41421-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
Health disparities are driven by underlying social disadvantage and psychosocial stressors. However, how social disadvantage and psychosocial stressors lead to adverse health outcomes is unclear, particularly when exposure begins prenatally. Variations in the gut microbiome and circulating proinflammatory cytokines offer potential mechanistic pathways. Here, we interrogate the gut microbiome of mother-child dyads to compare high-versus-low prenatal social disadvantage, psychosocial stressors and maternal circulating cytokine cohorts (prospective case-control study design using gut microbiomes from 121 dyads profiled with 16 S rRNA sequencing and 89 dyads with shotgun metagenomic sequencing). Gut microbiome characteristics significantly predictive of social disadvantage and psychosocial stressors in the mothers and children indicate that different discriminatory taxa and related pathways are involved, including many species of Bifidobacterium and related pathways across several comparisons. The lowest inter-individual gut microbiome similarity was observed among high-social disadvantage/high-psychosocial stressors mothers, suggesting distinct environmental exposures driving a diverging gut microbiome assembly compared to low-social disadvantage/low-psychosocial stressors controls (P = 3.5 × 10-5 for social disadvantage, P = 2.7 × 10-15 for psychosocial stressors). Children's gut metagenome profiles at 4 months also significantly predicted high/low maternal prenatal IL-6 (P = 0.029), with many bacterial species overlapping those identified by social disadvantage and psychosocial stressors. These differences, based on maternal social and psychological status during a critical developmental window early in life, offer potentially modifiable targets to mitigate health inequities.
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Affiliation(s)
- Barbara B Warner
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA.
| | - Bruce A Rosa
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - I Malick Ndao
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Phillip I Tarr
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - J Philip Miller
- Institute for Informatics, Data Science and Biostatistics, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Sarah K England
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Joan L Luby
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Cynthia E Rogers
- Departments of Psychiatry and Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Carla Hall-Moore
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Renay E Bryant
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Jacqueline D Wang
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Laura A Linneman
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Tara A Smyser
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Christopher D Smyser
- Departments of Neurology, Pediatrics and Radiology, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Deanna M Barch
- Department of Psychological and Brain Sciences, Psychiatry, & Radiology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Gregory E Miller
- Institute for Policy Research & Department of Psychology, Northwestern University, Evanston, IL, 60208, USA
| | - Edith Chen
- Institute for Policy Research & Department of Psychology, Northwestern University, Evanston, IL, 60208, USA
| | - John Martin
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Makedonka Mitreva
- Departments of Medicine and Genetics, and McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA.
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2
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Ferreiro AL, Choi J, Ryou J, Newcomer EP, Thompson R, Bollinger RM, Hall-Moore C, Ndao IM, Sax L, Benzinger TLS, Stark SL, Holtzman DM, Fagan AM, Schindler SE, Cruchaga C, Butt OH, Morris JC, Tarr PI, Ances BM, Dantas G. Gut microbiome composition may be an indicator of preclinical Alzheimer's disease. Sci Transl Med 2023; 15:eabo2984. [PMID: 37315112 PMCID: PMC10680783 DOI: 10.1126/scitranslmed.abo2984] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/26/2023] [Indexed: 06/16/2023]
Abstract
Alzheimer's disease (AD) pathology is thought to progress from normal cognition through preclinical disease and ultimately to symptomatic AD with cognitive impairment. Recent work suggests that the gut microbiome of symptomatic patients with AD has an altered taxonomic composition compared with that of healthy, cognitively normal control individuals. However, knowledge about changes in the gut microbiome before the onset of symptomatic AD is limited. In this cross-sectional study that accounted for clinical covariates and dietary intake, we compared the taxonomic composition and gut microbial function in a cohort of 164 cognitively normal individuals, 49 of whom showed biomarker evidence of early preclinical AD. Gut microbial taxonomic profiles of individuals with preclinical AD were distinct from those of individuals without evidence of preclinical AD. The change in gut microbiome composition correlated with β-amyloid (Aβ) and tau pathological biomarkers but not with biomarkers of neurodegeneration, suggesting that the gut microbiome may change early in the disease process. We identified specific gut bacterial taxa associated with preclinical AD. Inclusion of these microbiome features improved the accuracy, sensitivity, and specificity of machine learning classifiers for predicting preclinical AD status when tested on a subset of the cohort (65 of the 164 participants). Gut microbiome correlates of preclinical AD neuropathology may improve our understanding of AD etiology and may help to identify gut-derived markers of AD risk.
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Affiliation(s)
- Aura L. Ferreiro
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - JooHee Choi
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jian Ryou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Erin P. Newcomer
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Regina Thompson
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rebecca M. Bollinger
- Program in Occupational Therapy, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carla Hall-Moore
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - I. Malick Ndao
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laurie Sax
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tammie L. S. Benzinger
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan L. Stark
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Program in Occupational Therapy, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David M. Holtzman
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anne M. Fagan
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Suzanne E. Schindler
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carlos Cruchaga
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Omar H. Butt
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John C. Morris
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Phillip I. Tarr
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Beau M. Ances
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gautam Dantas
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
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3
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Schwartz DJ, Shalon N, Wardenburg K, DeVeaux A, Wallace MA, Hall-Moore C, Ndao IM, Sullivan JE, Radmacher P, Escobedo M, D. Burnham CA, Warner BB, Tarr PI, Dantas G. Gut pathogen colonization precedes bloodstream infection in the neonatal intensive care unit. Sci Transl Med 2023; 15:eadg5562. [PMID: 37134153 PMCID: PMC10259202 DOI: 10.1126/scitranslmed.adg5562] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023]
Abstract
Bacterial bloodstream infections (BSIs) resulting in late-onset sepsis affect up to half of extremely preterm infants and have substantial morbidity and mortality. Bacterial species associated with BSIs in neonatal intensive care units (NICUs) commonly colonize the preterm infant gut microbiome. Accordingly, we hypothesized that the gut microbiome is a reservoir of BSI-causing pathogenic strains that increase in abundance before BSI onset. We analyzed 550 previously published fecal metagenomes from 115 hospitalized neonates and found that recent ampicillin, gentamicin, or vancomycin exposure was associated with increased abundance of Enterobacteriaceae and Enterococcaceae in infant guts. We then performed shotgun metagenomic sequencing on 462 longitudinal fecal samples from 19 preterm infants (cases) with BSI and 37 non-BSI controls, along with whole-genome sequencing of the BSI isolates. Infants with BSI caused by Enterobacteriaceae were more likely than infants with BSI caused by other organisms to have had ampicillin, gentamicin, or vancomycin exposure in the 10 days before BSI. Relative to controls, gut microbiomes of cases had increased relative abundance of the BSI-causing species and clustered by Bray-Curtis dissimilarity according to BSI pathogen. We demonstrated that 11 of 19 (58%) of gut microbiomes before BSI, and 15 of 19 (79%) of gut microbiomes at any time, harbored the BSI isolate with fewer than 20 genomic substitutions. Last, BSI strains from the Enterobacteriaceae and Enterococcaceae families were detected in multiple infants, indicating BSI-strain transmission. Our findings support future studies to evaluate BSI risk prediction strategies based on gut microbiome abundance in hospitalized preterm infants.
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Affiliation(s)
- Drew J. Schwartz
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nitan Shalon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kate Wardenburg
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anna DeVeaux
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carla Hall-Moore
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - I. Malick Ndao
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janice E. Sullivan
- Department of Pediatrics, University of Louisville School of Medicine, Norton Children’s Hospital, Louisville, KY 40202, USA
| | - Paula Radmacher
- Department of Pediatrics, University of Louisville School of Medicine, Norton Children’s Hospital, Louisville, KY 40202, USA
| | - Marilyn Escobedo
- Department of Pediatrics, University of Oklahoma, Oklahoma City, OK 73117, USA
| | - Carey-Ann D. Burnham
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barbara B. Warner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Phillip I. Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gautam Dantas
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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4
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Kaelin EA, Rodriguez C, Hall-Moore C, Hoffmann JA, Linneman LA, Ndao IM, Warner BB, Tarr PI, Holtz LR, Lim ES. Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants. Nat Microbiol 2022; 7:653-662. [PMID: 35449461 PMCID: PMC9064801 DOI: 10.1038/s41564-022-01096-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/02/2022] [Indexed: 12/22/2022]
Abstract
Necrotizing enterocolitis (NEC) is a serious consequence of preterm birth and is often associated with gut bacterial microbiome alterations. However, little is known about the development of the gut virome in preterm infants, or its role in NEC. Here, using metagenomic sequencing, we characterized the DNA gut virome of 9 preterm infants who developed NEC and 14 gestational age-matched preterm infants who did not. Infants were sampled longitudinally before NEC onset over the first 11 weeks of life. We observed substantial interindividual variation in the gut virome between unrelated preterm infants, while intraindividual variation over time was significantly less. We identified viral and bacterial signatures in the gut that preceded NEC onset. Specifically, we observed a convergence towards reduced viral beta diversity over the 10 d before NEC onset, which was driven by specific viral signatures and accompanied by specific viral-bacterial interactions. Our results indicate that bacterial and viral perturbations precede the sudden onset of NEC. These findings suggest that early life virome signatures in preterm infants may be implicated in NEC.
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Affiliation(s)
- Emily A Kaelin
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.,Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Cynthia Rodriguez
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - Carla Hall-Moore
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - Julie A Hoffmann
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - Laura A Linneman
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - I Malick Ndao
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - Barbara B Warner
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - Phillip I Tarr
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.,Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Lori R Holtz
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
| | - Efrem S Lim
- School of Life Sciences, Arizona State University, Tempe, AZ, USA. .,Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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5
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Thänert R, Thänert A, Ou J, Bajinting A, Burnham CAD, Engelstad HJ, Tecos ME, Ndao IM, Hall-Moore C, Rouggly-Nickless C, Carl MA, Rubin DC, Davidson NO, Tarr PI, Warner BB, Dantas G, Warner BW. Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections. Gut Microbes 2021; 13:1940792. [PMID: 34264786 PMCID: PMC8284144 DOI: 10.1080/19490976.2021.1940792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 02/08/2023] Open
Abstract
Surgical removal of the intestine, lifesaving in catastrophic gastrointestinal disorders of infancy, can result in a form of intestinal failure known as short bowel syndrome (SBS). Bloodstream infections (BSIs) are a major challenge in pediatric SBS management. BSIs require frequent antibiotic therapy, with ill-defined consequences for the gut microbiome and childhood health. Here, we combine serial stool collection, shotgun metagenomic sequencing, multivariate statistics and genome-resolved strain-tracking in a cohort of 19 patients with surgically-induced SBS to show that antibiotic-driven intestinal dysbiosis in SBS enriches for persistent intestinal colonization with BSI causative pathogens in SBS. Comparing the gut microbiome composition of SBS patients over the first 4 years of life to 19 age-matched term and 18 preterm controls, we find that SBS gut microbiota diversity and composition was persistently altered compared to controls. Commensals including Ruminococcus, Bifidobacterium, Eubacterium, and Clostridium species were depleted in SBS, while pathobionts (Enterococcus) were enriched. Integrating clinical covariates with gut microbiome composition in pediatric SBS, we identified dietary and antibiotic exposures as the main drivers of these alterations. Moreover, antibiotic resistance genes, specifically broad-spectrum efflux pumps, were at a higher abundance in SBS, while putatively beneficial microbiota functions, including amino acid and vitamin biosynthesis, were depleted. Moreover, using strain-tracking we found that the SBS gut microbiome harbors BSI causing pathogens, which can persist intestinally throughout the first years of life. The association between antibiotic-driven gut dysbiosis and enrichment of intestinal pathobionts isolated from BSI suggests that antibiotic treatment may predispose SBS patients to infection. Persistence of pathobionts and depletion of beneficial microbiota and functionalities in SBS highlights the need for microbiota-targeted interventions to prevent infection and facilitate intestinal adaptation.
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Affiliation(s)
- Robert Thänert
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Anna Thänert
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jocelyn Ou
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Adam Bajinting
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Holly J. Engelstad
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Maria E. Tecos
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - I. Malick Ndao
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carla Hall-Moore
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Colleen Rouggly-Nickless
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mike A. Carl
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Deborah C. Rubin
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Nicholas O. Davidson
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Phillip I. Tarr
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Barbara B. Warner
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Brad W. Warner
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
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6
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Knoop KA, McDonald KG, Coughlin PE, Kulkarni DH, Gustafsson JK, Rusconi B, John V, Ndao IM, Beigelman A, Good M, Warner BB, Elson CO, Hsieh CS, Hogan SP, Tarr PI, Newberry RD. Synchronization of mothers and offspring promotes tolerance and limits allergy. JCI Insight 2020; 5:137943. [PMID: 32759496 DOI: 10.1172/jci.insight.137943] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
Allergic disorders, characterized by Th2 immune responses to environmental substances, are increasingly common in children in Western societies. Multiple studies indicate that breastfeeding, early complementary introduction of food allergens, and antibiotic avoidance in the first year of life reduces allergic outcomes in at-risk children. Why the benefit of these practices is restricted to early life is largely unknown. We identified a preweaning interval during which dietary antigens are assimilated by the colonic immune system. This interval is under maternal control via temporal changes in breast milk, coincides with an influx of naive T cells into the colon, and is followed by the development of a long-lived population of colonic peripherally derived Tregs (pTregs) that can be specific for dietary antigens encountered during this interval. Desynchronization of mothers and offspring produced durable deficits in these pTregs, impaired tolerance to dietary antigens introduced during and after this preweaning interval, and resulted in spontaneous Th2 responses. These effects could be rescued by pTregs from the periweaning colon or by Tregs generated in vitro using periweaning colonic antigen-presenting cells. These findings demonstrate that mothers and their offspring are synchronized for the development of a balanced immune system.
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Affiliation(s)
| | | | | | | | | | - Brigida Rusconi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - I Malick Ndao
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Avraham Beigelman
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.,The Kipper Institute of Allergy and Immunology, Schneider Children's Medical Center of Israel, Tel Aviv University, Israel
| | - Misty Good
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Barbara B Warner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Charles O Elson
- Department of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Simon P Hogan
- Mary H. Weiser Food Allergy Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Phillip I Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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7
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Knoop KA, Coughlin PE, Floyd AN, Ndao IM, Hall-Moore C, Shaikh N, Gasparrini AJ, Rusconi B, Escobedo M, Good M, Warner BB, Tarr PI, Newberry RD. Maternal activation of the EGFR prevents translocation of gut-residing pathogenic Escherichia coli in a model of late-onset neonatal sepsis. Proc Natl Acad Sci U S A 2020; 117:7941-7949. [PMID: 32179676 PMCID: PMC7148560 DOI: 10.1073/pnas.1912022117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Late-onset sepsis (LOS) is a highly consequential complication of preterm birth and is defined by a positive blood culture obtained after 72 h of age. The causative bacteria can be found in patients' intestinal tracts days before dissemination, and cohort studies suggest reduced LOS risk in breastfed preterm infants through unknown mechanisms. Reduced concentrations of epidermal growth factor (EGF) of maternal origin within the intestinal tract of mice correlated to the translocation of a gut-resident human pathogen Escherichia coli, which spreads systemically and caused a rapid, fatal disease in pups. Translocation of Escherichia coli was associated with the formation of colonic goblet cell-associated antigen passages (GAPs), which translocate enteric bacteria across the intestinal epithelium. Thus, maternally derived EGF, and potentially other EGFR ligands, prevents dissemination of a gut-resident pathogen by inhibiting goblet cell-mediated bacterial translocation. Through manipulation of maternally derived EGF and alteration of the earliest gut defenses, we have developed an animal model of pathogen dissemination which recapitulates gut-origin neonatal LOS.
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Affiliation(s)
- Kathryn A Knoop
- Department of Immunology, Mayo Clinic, Rochester, MN 55905;
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Paige E Coughlin
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Alexandria N Floyd
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - I Malick Ndao
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Carla Hall-Moore
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Nurmohammad Shaikh
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Andrew J Gasparrini
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110
| | - Brigida Rusconi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Marilyn Escobedo
- Department of Pediatrics, University of Oklahoma School of Medicine, Oklahoma City, OK 73019
| | - Misty Good
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Barbara B Warner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Phillip I Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - Rodney D Newberry
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110
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8
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Liu TC, VanBuskirk K, Ali SA, Kelly MP, Holtz LR, Yilmaz OH, Sadiq K, Iqbal N, Amadi B, Syed S, Ahmed T, Moore S, Ndao IM, Isaacs MH, Pfeifer JD, Atlas H, Tarr PI, Denno DM, Moskaluk CA. A novel histological index for evaluation of environmental enteric dysfunction identifies geographic-specific features of enteropathy among children with suboptimal growth. PLoS Negl Trop Dis 2020; 14:e0007975. [PMID: 31929525 PMCID: PMC6980693 DOI: 10.1371/journal.pntd.0007975] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 01/24/2020] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Background A major limitation to understanding the etiopathogenesis of environmental enteric dysfunction (EED) is the lack of a comprehensive, reproducible histologic framework for characterizing the small bowel lesions. We hypothesized that the development of such a system will identify unique histology features for EED, and that some features might correlate with clinical severity. Methods Duodenal endoscopic biopsies from two cohorts where EED is prevalent (Pakistan, Zambia) and North American children with and without gluten sensitive enteropathy (GSE) were processed for routine hematoxylin & eosin (H&E) staining, and scanned to produce whole slide images (WSIs) which we shared among study pathologists via a secure web browser-based platform. A semi-quantitative scoring index composed of 11 parameters encompassing tissue injury and response patterns commonly observed in routine clinical practice was constructed by three gastrointestinal pathologists, with input from EED experts. The pathologists then read the WSIs using the EED histology index, and inter-observer reliability was assessed. The histology index was further used to identify within- and between-child variations as well as features common across and unique to each cohort, and those that correlated with host phenotype. Results Eight of the 11 histologic scoring parameters showed useful degrees of variation. The overall concordance across all parameters was 96% weighted agreement, kappa 0.70, and Gwet’s AC 0.93. Zambian and Pakistani tissues shared some histologic features with GSE, but most features were distinct, particularly abundance of intraepithelial lymphocytes in the Pakistani cohort, and marked villous destruction and loss of secretory cell lineages in the Zambian cohort. Conclusions We propose the first EED histology index for interpreting duodenal biopsies. This index should be useful in future clinical and translational studies of this widespread, poorly understood, and highly consequential disorder, which might be caused by multiple contributing processes, in different regions of the world. The study of EED has been limited by the lack of a rigorously tested, reproducible histology index that can provide insight to the pathogenesis of this entity. In this study we report the first duodenal histology index that was developed using an unbiased approach, with excellent inter-observer reproducibility, for the study of EED. The EED histology index readily identified histologic features that are common or unique to cohorts of distinct geographic locations. Incorporating the histology index into future clinical studies will provide useful insight into the pathogenesis and for intervention strategy development.
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Affiliation(s)
- Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Kelley VanBuskirk
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Syed A. Ali
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - M. Paul Kelly
- Tropical Gastroenterology and Nutrition group, University of Zambia School of Medicine, Lusaka, Zambia
- Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, London, United Kingdom
| | - Lori R. Holtz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Omer H. Yilmaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, Department of Pathology, Massachusetts General Hospital, Boston, MA, United States of America
| | - Kamran Sadiq
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Najeeha Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Beatrice Amadi
- Tropical Gastroenterology and Nutrition group, University of Zambia School of Medicine, Lusaka, Zambia
| | - Sana Syed
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Department of Pediatrics, University of Virginia, Charlottesville, VA, United States of America
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
- James P. Grant School of Public Health, BRAC University, Dhaka, Bangladesh
| | - Sean Moore
- Department of Pediatrics, University of Virginia, Charlottesville, VA, United States of America
| | - I. Malick Ndao
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Michael H. Isaacs
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - John D. Pfeifer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Hannah Atlas
- Departments of Pediatrics and Global Health, University of Washington, Seattle, WA, United States of America
| | - Phillip I. Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Donna M. Denno
- Departments of Pediatrics and Global Health, University of Washington, Seattle, WA, United States of America
| | - Christopher A. Moskaluk
- Department of Pathology, University of Virginia, Charlottesville, VA, United States of America
- * E-mail:
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9
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Maqsood R, Rodgers R, Rodriguez C, Handley SA, Ndao IM, Tarr PI, Warner BB, Lim ES, Holtz LR. Discordant transmission of bacteria and viruses from mothers to babies at birth. Microbiome 2019; 7:156. [PMID: 31823811 PMCID: PMC6902606 DOI: 10.1186/s40168-019-0766-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/08/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND The earliest microbial colonizers of the human gut can have life-long consequences for their hosts. Precisely how the neonatal gut bacterial microbiome and virome are initially populated is not well understood. To better understand how the maternal gut microbiome influences acquisition of the infant gut microbiome, we studied the early life bacterial microbiomes and viromes of 28 infant twin pairs and their mothers. RESULTS Infant bacterial and viral communities more closely resemble those of their related co-twin than unrelated infants. We found that 63% of an infant's bacterial microbiome can be traced to their mother's gut microbiota. In contrast, only 15% of their viral communities are acquired from their mother. Delivery route did not determine how much of the bacterial microbiome or virome was shared from mother to infant. However, bacteria-bacteriophage interactions were altered by delivery route. CONCLUSIONS The maternal gut microbiome significantly influences infant gut microbiome acquisition. Vertical transmission of the bacterial microbiome is substantially higher compared to vertical transmission of the virome. However, the degree of similarity between the maternal and infant gut bacterial microbiome and virome did not vary by delivery route. The greater similarity of the bacterial microbiome and virome between twin pairs than unrelated twins may reflect a shared environmental exposure. Thus, differences of the inter-generation transmissibility at birth between the major kingdoms of microbes indicate that the foundation of these microbial communities are shaped by different rules. Video Abstract.
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Affiliation(s)
- Rabia Maqsood
- School of Life Sciences, Arizona State University, Tempe, AZ 85287 USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Tempe, AZ 85287 USA
| | - Rachel Rodgers
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Cynthia Rodriguez
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Scott A. Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - I. Malick Ndao
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Phillip I. Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Barbara B. Warner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Efrem S. Lim
- School of Life Sciences, Arizona State University, Tempe, AZ 85287 USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Tempe, AZ 85287 USA
| | - Lori R. Holtz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110 USA
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10
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Gasparrini AJ, Wang B, Sun X, Kennedy EA, Hernandez-Leyva A, Ndao IM, Tarr PI, Warner BB, Dantas G. Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome. Nat Microbiol 2019; 4:2285-2297. [PMID: 31501537 PMCID: PMC6879825 DOI: 10.1038/s41564-019-0550-2] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 07/26/2019] [Indexed: 12/29/2022]
Abstract
Hospitalized preterm infants receive frequent and often prolonged exposures to antibiotics because they are vulnerable to infection. It is not known whether the short-term effects of antibiotics on the preterm infant gut microbiota and resistome persist after discharge from neonatal intensive care units. Here, we use complementary metagenomic, culture-based and machine learning techniques to study the gut microbiota and resistome of antibiotic-exposed preterm infants during and after hospitalization, and we compare these readouts to antibiotic-naive healthy infants sampled synchronously. We find a persistently enriched gastrointestinal antibiotic resistome, prolonged carriage of multidrug-resistant Enterobacteriaceae and distinct antibiotic-driven patterns of microbiota and resistome assembly in extremely preterm infants that received early-life antibiotics. The collateral damage of early-life antibiotic treatment and hospitalization in preterm infants is long lasting. We urge the development of strategies to reduce these consequences in highly vulnerable neonatal populations.
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Affiliation(s)
- Andrew J Gasparrini
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Xiaoqing Sun
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Elizabeth A Kennedy
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Ariel Hernandez-Leyva
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - I Malick Ndao
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Phillip I Tarr
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Barbara B Warner
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University in St Louis School of Medicine, St Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO, USA.
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11
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Chama M, Amadi BC, Chandwe K, Zyambo K, Besa E, Shaikh N, Ndao IM, Tarr PI, Storer C, Head R, Kelly P. Transcriptomic analysis of enteropathy in Zambian children with severe acute malnutrition. EBioMedicine 2019; 45:456-463. [PMID: 31229436 PMCID: PMC6642221 DOI: 10.1016/j.ebiom.2019.06.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/11/2019] [Accepted: 06/11/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Children with severe acute malnutrition (SAM), with or without diarrhoea, often have enteropathy, but there are few molecular data to guide development of new therapies. We set out to determine whether SAM enteropathy is characterised by specific transcriptional changes which might improve understanding or help identify new treatments. METHODS We collected intestinal biopsies from children with SAM and persistent diarrhoea. mRNA was extracted from biopsies, sequenced, and subjected to a progressive set of complementary analytical approaches: NOIseq, Gene Set Enrichment Analysis (GSEA), and correlation analysis of phenotypic data with gene expression. FINDINGS Transcriptomic profiles were generated for biopsy sets from 27 children of both sexes, under 2 years of age, of whom one-third were HIV-infected. NOIseq analysis, constructed from phenotypic group extremes, revealed 66 differentially expressed genes (DEGs) out of 21,386 mapped to the reference genome. These DEGs include genes for mucins and mucus integrity, antimicrobial defence, nutrient absorption, C-X-C chemokines, proteases and anti-proteases. Phenotype - expression correlation analysis identified 1221 genes related to villus height, including increased cell cycling gene expression in more severe enteropathy. Amino acid transporters and ZIP zinc transporters were specifically increased in severe enteropathy, but transcripts for xenobiotic metabolising enzymes were reduced. INTERPRETATION Transcriptomic analysis of this rare collection of intestinal biopsies identified multiple novel elements of pathology, including specific alterations in nutrient transporters. Changes in xenobiotic metabolism in the gut may alter drug disposition. Both NOIseq and GSEA identified gene clusters similar to those differentially expressed in pediatric Crohn's disease but to a much lesser degree than those identified in coeliac disease. FUND: Bill & Melinda Gates Foundation OPP1066118. The funding agency had no role in study design, data collection, data analysis, interpretation, or writing of the report.
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Affiliation(s)
- Mubanga Chama
- Tropical Gastroenterology and Nutrition group, University of Zambia School of Medicine, Nationalist Road, Lusaka, Zambia
| | - Beatrice C Amadi
- Tropical Gastroenterology and Nutrition group, University of Zambia School of Medicine, Nationalist Road, Lusaka, Zambia
| | - Kanta Chandwe
- Tropical Gastroenterology and Nutrition group, University of Zambia School of Medicine, Nationalist Road, Lusaka, Zambia
| | - Kanekwa Zyambo
- Tropical Gastroenterology and Nutrition group, University of Zambia School of Medicine, Nationalist Road, Lusaka, Zambia
| | - Ellen Besa
- Tropical Gastroenterology and Nutrition group, University of Zambia School of Medicine, Nationalist Road, Lusaka, Zambia
| | - Nurmohammad Shaikh
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, United States
| | - I Malick Ndao
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, United States
| | - Philip I Tarr
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, United States
| | - Chad Storer
- Department of Genetics, Washington University School of Medicine, St Louis, MO, United States
| | - Richard Head
- Department of Genetics, Washington University School of Medicine, St Louis, MO, United States
| | - Paul Kelly
- Tropical Gastroenterology and Nutrition group, University of Zambia School of Medicine, Nationalist Road, Lusaka, Zambia; Blizard Institute, Barts & The London School of Medicine, Queen Mary University of London, 4 Newark Street, London, UK.
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12
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Warner BB, Deych E, Zhou Y, Hall-Moore C, Weinstock GM, Sodergren E, Shaikh N, Hoffmann JA, Linneman LA, Hamvas A, Khanna G, Rouggly-Nickless LC, Ndao IM, Shands BA, Escobedo M, Sullivan JE, Radmacher PG, Shannon WD, Tarr PI. Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: a prospective case-control study. Lancet 2016; 387:1928-36. [PMID: 26969089 PMCID: PMC5553277 DOI: 10.1016/s0140-6736(16)00081-7] [Citation(s) in RCA: 300] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Gut bacteria might predispose to or protect from necrotising enterocolitis, a severe illness linked to prematurity. In this observational prospective study we aimed to assess whether one or more bacterial taxa in the gut differ between infants who subsequently develop necrotising enterocolitis (cases) and those who do not (controls). METHODS We enrolled very low birthweight (1500 g and lower) infants in the primary cohort (St Louis Children's Hospital) between July 7, 2009, and Sept 16, 2013, and in the secondary cohorts (Kosair Children's Hospital and Children's Hospital at Oklahoma University) between Sept 12, 2011 and May 25, 2013. We prospectively collected and then froze stool samples for all infants. Cases were defined as infants whose clinical courses were consistent with necrotising enterocolitis and whose radiographs fulfilled criteria for Bell's stage 2 or 3 necrotising enterocolitis. Control infants (one to four per case; not fixed ratios) with similar gestational ages, birthweight, and birth dates were selected from the population after cases were identified. Using primers specific for bacterial 16S rRNA genes, we amplified and then pyrosequenced faecal DNA from stool samples. With use of Dirichlet multinomial analysis and mixed models to account for repeated measures, we identified host factors, including development of necrotising enterocolitis, associated with gut bacterial populations. FINDINGS We studied 2492 stool samples from 122 infants in the primary cohort, of whom 28 developed necrotising enterocolitis; 94 infants were used as controls. The microbial community structure in case stools differed significantly from those in control stools. These differences emerged only after the first month of age. In mixed models, the time-by-necrotising-enterocolitis interaction was positively associated with Gammaproteobacteria (p=0·0010) and negatively associated with strictly anaerobic bacteria, especially Negativicutes (p=0·0019). We studied 1094 stool samples from 44 infants in the secondary cohorts. 18 infants developed necrotising enterocolitis (cases) and 26 were controls. After combining data from all cohorts (166 infants, 3586 stools, 46 cases of necrotising enterocolitis), there were increased proportions of Gammaproteobacteria (p=0·0011) and lower proportions of both Negativicutes (p=0·0013) and the combined Clostridia-Negativicutes class (p=0·0051) in infants who went on to develop necrotising enterocolitis compared with controls. These associations were strongest in both the primary cohort and the overall cohort for infants born at less than 27 weeks' gestation. INTERPRETATION A relative abundance of Gammaproteobacteria (ie, Gram-negative facultative bacilli) and relative paucity of strict anaerobic bacteria (especially Negativicutes) precede necrotising enterocolitis in very low birthweight infants. These data offer candidate targets for interventions to prevent necrotising enterocolitis, at least among infants born at less than 27 weeks' gestation. FUNDING National Institutes of Health (NIH), Foundation for the NIH, the Children's Discovery Institute.
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Affiliation(s)
- Barbara B Warner
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Elena Deych
- Department of Medicine, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Yanjiao Zhou
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Carla Hall-Moore
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - George M Weinstock
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Erica Sodergren
- McDonnell Genome Institute, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Nurmohammad Shaikh
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Julie A Hoffmann
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Laura A Linneman
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Aaron Hamvas
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Geetika Khanna
- Department of Radiology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | | | - I Malick Ndao
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Berkley A Shands
- Department of Medicine, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Marilyn Escobedo
- Department of Pediatrics, University of Oklahoma School of Medicine, Oklahoma City, OK, USA
| | - Janice E Sullivan
- Department of Pediatrics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Paula G Radmacher
- Department of Pediatrics, University of Louisville School of Medicine, Louisville, KY, USA
| | - William D Shannon
- Department of Medicine, Washington University in St Louis School of Medicine, St Louis, MO, USA.
| | - Phillip I Tarr
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA; Department of Molecular Microbiology, Washington University in St Louis School of Medicine, St Louis, MO, USA.
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13
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Lim ES, Zhou Y, Zhao G, Bauer IK, Droit L, Ndao IM, Warner BB, Tarr PI, Wang D, Holtz LR. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat Med 2015; 21:1228-34. [PMID: 26366711 DOI: 10.1038/nm.3950] [Citation(s) in RCA: 398] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/20/2015] [Indexed: 12/13/2022]
Abstract
The early years of life are important for immune development and influence health in adulthood. Although it has been established that the gut bacterial microbiome is rapidly acquired after birth, less is known about the viral microbiome (or 'virome'), consisting of bacteriophages and eukaryotic RNA and DNA viruses, during the first years of life. Here, we characterized the gut virome and bacterial microbiome in a longitudinal cohort of healthy infant twins. The virome and bacterial microbiome were more similar between co-twins than between unrelated infants. From birth to 2 years of age, the eukaryotic virome and the bacterial microbiome expanded, but this was accompanied by a contraction of and shift in the bacteriophage virome composition. The bacteriophage-bacteria relationship begins from birth with a high predator-low prey dynamic, consistent with the Lotka-Volterra prey model. Thus, in contrast to the stable microbiome observed in adults, the infant microbiome is highly dynamic and associated with early life changes in the composition of bacteria, viruses and bacteriophages with age.
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Affiliation(s)
- Efrem S Lim
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pathology &Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Yanjiao Zhou
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Guoyan Zhao
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Irma K Bauer
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lindsay Droit
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pathology &Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - I Malick Ndao
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Barbara B Warner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Phillip I Tarr
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - David Wang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pathology &Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lori R Holtz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
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14
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Gurnee EA, Ndao IM, Johnson JR, Johnston BD, Gonzalez MD, Burnham CAD, Hall-Moore CM, McGhee JE, Mellmann A, Warner BB, Tarr PI. Gut Colonization of Healthy Children and Their Mothers With Pathogenic Ciprofloxacin-Resistant Escherichia coli. J Infect Dis 2015; 212:1862-8. [PMID: 25969564 DOI: 10.1093/infdis/jiv278] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/21/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The reservoir of pathogenic ciprofloxacin-resistant Escherichia coli remains unknown. METHODS We conducted a prospective cohort study of 80 healthy twins and their mothers to determine the frequency of excretion of ciprofloxacin-resistant, potentially pathogenic E. coli. Stool specimens were cultured selectively for ciprofloxacin-resistant gram-negative bacteria. Isolates were categorized on the basis of additional resistance and virulence profiles. We also prospectively collected clinical metadata. RESULTS Fifteen children (19%) and 8 mothers (20%) excreted ciprofloxacin-resistant E. coli at least once. Overall, 33% of 40 families had at least 1 member whose stool specimen yielded ciprofloxacin-resistant E. coli on culture. Fifty-seven submitted stool specimens (2.8%) contained such organisms; clones ST131-H30 and ST405 accounted for 52 and 5 of the positive specimens, respectively. Length of hospital stay after birth (P = .002) and maternal colonization (P = .0001) were associated with subsequent childhood carriage of ciprofloxacin-resistant E. coli; antibiotic use, acid suppression, sex, mode of delivery, and maternal perinatal antibiotic use were not. Ciprofloxacin-resistant E. coli were usually resistant to additional antibiotic classes, and all had virulence genotypes typical of extraintestinal pathogenic E. coli. CONCLUSIONS Healthy children and their mothers commonly harbor ciprofloxacin-resistant E. coli with pathogenic potential.
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Affiliation(s)
| | | | - James R Johnson
- Minneapolis Veterans Affairs Medical Center Department of Medicine, University of Minnesota, Minneapolis
| | - Brian D Johnston
- Minneapolis Veterans Affairs Medical Center Department of Medicine, University of Minnesota, Minneapolis
| | - Mark D Gonzalez
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | | | | | | | | | - Phillip I Tarr
- Department of Pediatrics Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri
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15
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Moore AM, Ahmadi S, Patel S, Gibson MK, Wang B, Ndao IM, Deych E, Shannon W, Tarr PI, Warner BB, Dantas G. Erratum: Gut resistome development in healthy twin pairs in the first year of life. Microbiome 2015; 3:29. [PMID: 26207183 PMCID: PMC4511998 DOI: 10.1186/s40168-015-0095-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 07/07/2015] [Indexed: 05/17/2023]
Abstract
[This corrects the article DOI: 10.1186/s40168-015-0090-9.].
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Affiliation(s)
- Aimee M. Moore
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Sara Ahmadi
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Sanket Patel
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Molly K. Gibson
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Bin Wang
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - I. Malick Ndao
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Elena Deych
- />Department of Biostatistics, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - William Shannon
- />Department of Biostatistics, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Phillip I. Tarr
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Department of Molecular Microbiology, Washington University in St. School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Barbara B. Warner
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Gautam Dantas
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
- />Department of Biomedical Engineering, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130 USA
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16
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Carl MA, Ndao IM, Springman AC, Manning SD, Johnson JR, Johnston BD, Burnham CAD, Weinstock ES, Weinstock GM, Wylie TN, Mitreva M, Abubucker S, Zhou Y, Stevens HJ, Hall-Moore C, Julian S, Shaikh N, Warner BB, Tarr PI. Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections. Clin Infect Dis 2014; 58:1211-8. [PMID: 24647013 DOI: 10.1093/cid/ciu084] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Late-onset sepsis is a major problem in neonatology, but the habitat of the pathogens before bloodstream invasion occurs is not well established. METHODS We examined prospectively collected stools from premature infants with sepsis to find pathogens that subsequently invaded their bloodstreams, and sought the same organisms in stools of infants without sepsis. Culture-based techniques were used to isolate stool bacteria that provisionally matched the bloodstream organisms, which were then genome sequenced to confirm or refute commonality. RESULTS Of 11 children with late-onset neonatal bloodstream infections, 7 produced at least 1 stool that contained group B Streptococcus (GBS), Serratia marcescens, or Escherichia coli before their sepsis episode with provisionally matching organisms. Of 96 overlap comparison subjects without sepsis temporally associated with these cases, 4 were colonized with provisionally matching GBS or S. marcescens. Of 175 comparisons of stools from randomly selected infants without sepsis, 1 contained a GBS (this infant had also served as an overlap comparison subject and both specimens contained provisionally matching GBS). Genome sequencing confirmed common origin of provisionally matching fecal and blood isolates. The invasive E. coli were present in all presepticemic stools since birth, but gut colonization with GBS and S. marcescens occurred closer to time of bloodstream infection. CONCLUSIONS The neonatal gut harbors sepsis-causing pathogens, but such organisms are not inevitable members of the normal microbiota. Surveillance microbiology, decolonization, and augmented hygiene might prevent dissemination of invasive bacteria between and within premature infants.
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Affiliation(s)
- Mike A Carl
- Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri
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